In bioscience research, medical treatment, drug development and similar fields, it has become increasingly important to examine biological samples to comprehensively identify various substances, such as proteins, peptides, nucleic acids and sugar chains. In particular, when aimed at proteins or peptides, such a comprehensive analysis method is called “shotgun proteomics.” For such analyses, the combination of a liquid chromatography and an MSn mass spectrometer (tandem mass spectrometer) has proven itself to be a very powerful technique.
As a mass spectrometer used for the previously described purposes (any type of mass spectrometer, including an MSn mass spectrometer, is hereinafter simply called the mass spectrometer), an ESI-MS having an electrospray ionization (ESI) source or a MALDI-MS having a MALDI ion source is used. In the case of an LC/ESI-MS, i.e. the combination of an LC and an ESI-MS, since the components in a liquid sample can be directly ionized, the introduction of the sample from the LC into the MS has been automatized. By contrast, the LC/MALDI-MS, i.e. the combination of an LC and a MALDI-MS, requires a larger amount of workload of analysis operators than the LC/ESI-MS since it requires the task of preparative-separating and fractionating sample components separated by the LC and placing spots of fractionated samples onto a sample plate. The workload for such a task can be reduced, for example, by using an automatic sample-dropping device described in Patent Literature 1.
For a comprehensive analysis of biological samples containing a number of components and having a wide dynamic range (i.e. with a wide range of component concentrations), it is necessary to achieve a high level of separatory capability in the LC. Attempts have been made for that purpose, such as a multi-dimensional separation using various separation modes combined together (see Non-Patent literatures 1 and 2) or a prolonged analysis using a meter-long monolithic silica column (see Non-Patent Literature 3). By using such LC techniques with high levels of separatory capability, the number of components contained in each fractionated sample can be reduced and a high-quality mass spectrum with a smaller amount of noise factors can be obtained. However, a problem exists in that a large number of fractionated samples need to be prepared, so that the analytical measurement time (i.e. the period of time for performing a mass spectrometry of the fractionated samples and collecting data) will be long. Furthermore, since an enormous amount of mass spectrum data are obtained through the mass spectrometry, an extremely long period of time is required for the data analysis. In particular, in the case of the LC/MALDI-MS, which has the LC and the MALDI-MS connected offline, an increase in the number of fractionated samples to be individually placed on a sample plate almost directly leads to an increase in the entire analysis time (see Non-Patent Literature 4).
Therefore, although a high level of LC-separatory capability has been achieved, it is inevitable to limit the number of fractionations taking into account the limitation of the analytical measurement time and the data analysis time. As a result, a plurality of components (in particular, an impurity that is unrelated to the analysis) may be mixed in one fractionated sample, which lowers the accuracy of the analysis.
In a system described in Patent Literature 2, the enormous amount of data obtained by an LC/MS or LC/MS/MS analysis is reduced to a smaller amount of data before an analyzing process in such a manner that the data which can be regarded as originating from a known sample yet being out of interest are removed based on the retention time in the LC, the mass value in the MS and/or other clues, leaving only such data that possibly contain new findings. This technique can reduce the amount of data to be analyzed but cannot shorten the period of time required for the original analytical measurement. There also remains the problem that the enormous amount of data collected through the analysis need to be temporarily stored in a memory or other storage devices and it is necessary to ensure a sufficient memory capacity for that purpose.